@apollo-annotation/jbrowse-plugin-apollo 0.1.5 → 0.1.7

package/dist/index.esm.js

@@ -48,7 +48,7 @@ import ExpandLessIcon from '@mui/icons-material/ExpandLess';
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 import ErrorIcon from '@mui/icons-material/Error';
 
-var version = "0.1.5";
+var version = "0.1.7";
 
 const ApolloConfigSchema = ConfigurationSchema('ApolloInternetAccount', {
     baseURL: {
@@ -120,7 +120,7 @@ async function checkFeatures(assembly) {
     for (const ref of assembly.refSeqs.values()) {
         for (const feature of ref.features.values()) {
             for (const check of checkRegistry.getChecks().values()) {
-                const result = await check.checkFeature(getSnapshot(feature), async (start, stop) => ref.getSequence(start, stop));
+                const result = await check.checkFeature(getSnapshot(feature), (start, stop) => Promise.resolve(ref.getSequence(start, stop)));
                 checkResults.push(...result);
             }
         }
@@ -212,14 +212,14 @@ function createFeature(gff3Feature) {
             }
         }
     }
-    if (childFeatures?.length) {
+    if (childFeatures.length > 0) {
         const children = {};
         for (const childFeature of childFeatures) {
             const child = createFeature(childFeature);
             children[child._id] = child;
             // Add value to gffId
             child.attributes?._id
-                ? (child.gffId = child.attributes?._id.toString())
+                ? (child.gffId = child.attributes._id.toString())
                 : (child.gffId = child._id);
         }
         feature.children = children;
@@ -321,6 +321,7 @@ function getApolloInternetAccount(session) {
     return internetAccounts.find((ia) => ia.type === 'ApolloInternetAccount');
 }
 
+/* eslint-disable @typescript-eslint/unbound-method */
 const useStyles$f = makeStyles()((theme) => ({
     dialogTitle: {
         background: theme.palette.primary.main,
@@ -343,6 +344,7 @@ const Dialog = observer(function JBrowseDialog(props) {
                 React__default.createElement(CloseIcon, null))) }));
 });
 
+/* eslint-disable @typescript-eslint/no-unsafe-enum-comparison */
 var FileType;
 (function (FileType) {
     FileType["GFF3"] = "text/x-gff3";
@@ -550,21 +552,29 @@ function AddAssembly({ changeManager, handleClose, session, }) {
                         React__default.createElement(FormControlLabel, { value: FileType.EXTERNAL, control: React__default.createElement(Radio, null), label: "External", disabled: submitted && !errorMessage }))),
                 fileType === FileType.EXTERNAL ? (React__default.createElement(Box, { style: { marginTop: 20 } },
                     React__default.createElement(Typography, { variant: "caption" }, "Enter FASTA and FASTA index(es) URL"),
-                    React__default.createElement(TextField, { margin: "dense", helperText: "Can be bgz-compressed", id: "fasta", label: "FASTA", type: "TextField", fullWidth: true, variant: "outlined", error: !validFastaFile, onChange: (e) => setFastaFile(e.target.value), disabled: submitted && !errorMessage, InputProps: {
+                    React__default.createElement(TextField, { margin: "dense", helperText: "Can be bgz-compressed", id: "fasta", label: "FASTA", type: "TextField", fullWidth: true, variant: "outlined", error: !validFastaFile, onChange: (e) => {
+                            setFastaFile(e.target.value);
+                        }, disabled: submitted && !errorMessage, InputProps: {
                             startAdornment: (React__default.createElement(InputAdornment, { position: "start" },
                                 React__default.createElement(LinkIcon, null))),
                         } }),
-                    React__default.createElement(TextField, { margin: "dense", id: "fasta-index", label: "FASTA Index", helperText: ".fai or .gz.fai", type: "TextField", fullWidth: true, variant: "outlined", error: !validFastaIndexFile, onChange: (e) => setFastaIndexFile(e.target.value), disabled: submitted && !errorMessage, InputProps: {
+                    React__default.createElement(TextField, { margin: "dense", id: "fasta-index", label: "FASTA Index", helperText: ".fai or .gz.fai", type: "TextField", fullWidth: true, variant: "outlined", error: !validFastaIndexFile, onChange: (e) => {
+                            setFastaIndexFile(e.target.value);
+                        }, disabled: submitted && !errorMessage, InputProps: {
                             startAdornment: (React__default.createElement(InputAdornment, { position: "start" },
                                 React__default.createElement(LinkIcon, null))),
                         } }),
-                    React__default.createElement(TextField, { margin: "dense", id: "fasta-gzi-index", label: "FASTA GZI Index", helperText: "Only for bgz-compressed FASTA, .gz.gzi", type: "TextField", fullWidth: true, variant: "outlined", error: Boolean(fastaGziIndexFile) && !validFastaGziIndexFile, onChange: (e) => setFastaGziIndexFile(e.target.value), disabled: submitted && !errorMessage, InputProps: {
+                    React__default.createElement(TextField, { margin: "dense", id: "fasta-gzi-index", label: "FASTA GZI Index", helperText: "Only for bgz-compressed FASTA, .gz.gzi", type: "TextField", fullWidth: true, variant: "outlined", error: Boolean(fastaGziIndexFile) && !validFastaGziIndexFile, onChange: (e) => {
+                            setFastaGziIndexFile(e.target.value);
+                        }, disabled: submitted && !errorMessage, InputProps: {
                             startAdornment: (React__default.createElement(InputAdornment, { position: "start" },
                                 React__default.createElement(LinkIcon, null))),
                         } }))) : (React__default.createElement(Box, { style: { marginTop: 20 } },
                     React__default.createElement("input", { type: "file", onChange: handleChangeFile, disabled: submitted && !errorMessage }),
                     React__default.createElement(FormGroup, null,
-                        React__default.createElement(FormControlLabel, { control: React__default.createElement(Checkbox, { checked: fileType === FileType.GFF3 && importFeatures, onChange: () => setImportFeatures(!importFeatures), disabled: fileType !== FileType.GFF3 ||
+                        React__default.createElement(FormControlLabel, { control: React__default.createElement(Checkbox, { checked: fileType === FileType.GFF3 && importFeatures, onChange: () => {
+                                    setImportFeatures(!importFeatures);
+                                }, disabled: fileType !== FileType.GFF3 ||
                                     (submitted && !errorMessage) }), label: "Also load features from GFF3 file" }))))),
             React__default.createElement(DialogActions, null,
                 React__default.createElement(Button, { disabled: !validAsm ||
@@ -751,7 +761,7 @@ function expandPrefixes(uri, prefixes) {
     return uri;
 }
 
-/* eslint-disable import/no-named-as-default-member */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 /** special value of jsonPath that gets the IRI (that is, ID) of the node with the configured prefixes applied */
 const PREFIXED_ID_PATH = '$PREFIXED_ID';
 /** small wrapper for jsonpath.query that intercepts requests for the special prefixed ID path */
@@ -935,6 +945,7 @@ function isDeprecated(thing) {
     return Boolean(thing.meta?.deprecated);
 }
 
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /** schema version we are currently on, used for the IndexedDB schema open call */
 const schemaVersion = 2;
 /** open the IndexedDB and create the DB schema if necessary */
@@ -1064,10 +1075,11 @@ async function isDatabaseCurrent(db) {
         return false;
     }
     // check that the index paths and prefixes are the same as our current ones
-    return (equal(this.options.prefixes, meta.storeOptions?.prefixes) &&
-        equal(this.options.textIndexing, meta.storeOptions?.textIndexing));
+    return (equal(this.options.prefixes, meta.storeOptions.prefixes) &&
+        equal(this.options.textIndexing, meta.storeOptions.textIndexing));
 }
 
+/* eslint-disable @typescript-eslint/no-throw-literal */
 /**
  * @deprecated use the one from jbrowse core when it is published
  **/
@@ -1162,7 +1174,7 @@ class OntologyStore {
         const myTx = tx ?? db.transaction('nodes');
         return myTx.objectStore('nodes').count();
     }
-    async unique(nodes) {
+    unique(nodes) {
         const seen = new Map();
         const result = [];
         for (const node of nodes) {
@@ -1227,10 +1239,7 @@ class OntologyStore {
         const resultIds = new Set();
         async function recur(queryIds) {
             await Promise.all([...queryIds].map(async (queryId) => {
-                const theseResults = (await myTx
-                    .objectStore('edges')
-                    .index(queryIndex)
-                    .getAll(queryId))
+                const theseResults = (await myTx.objectStore('edges').index(queryIndex).getAll(queryId))
                     .filter((element) => filterEdge(element))
                     .map((edge) => edge[resultProp]);
                 if (theseResults.length > 0) {
@@ -1497,13 +1506,13 @@ async function fetchValidDescendantTerms(parentFeature, ontologyStore, _signal)
     return subpartTerms;
 }
 
+/* eslint-disable @typescript-eslint/no-unused-vars */
 function OntologyTermAutocomplete({ fetchValidTerms, filterTerms: filterTermsProp, includeDeprecated, onChange, ontologyName, ontologyVersion, renderInput, session, style, value: valueString, }) {
     const [open, setOpen] = useState(false);
     const [termChoices, setTermChoices] = useState();
     const [currentOntologyTermInvalid, setCurrentOntologyTermInvalid] = useState('');
     const [currentOntologyTerm, setCurrentOntologyTerm] = useState();
-    const ontologyManager = session.apolloDataStore
-        .ontologyManager;
+    const { ontologyManager } = session.apolloDataStore;
     const ontologyStore = ontologyManager.findOntology(ontologyName, ontologyVersion)?.dataStore;
     const needToLoadTermChoices = ontologyStore && open && !termChoices;
     const needToLoadCurrentTerm = ontologyStore && !currentOntologyTerm;
@@ -1563,7 +1572,7 @@ function OntologyTermAutocomplete({ fetchValidTerms, filterTerms: filterTermsPro
         session,
         fetchValidTerms,
     ]);
-    const handleChange = async (event, newValue) => {
+    const handleChange = (event, newValue) => {
         if (!newValue) {
             return;
         }
@@ -1669,7 +1678,7 @@ function AddChildFeature({ changeManager, handleClose, session, sourceAssemblyId
             },
             parentFeatureId: sourceFeature._id,
         });
-        await changeManager.submit?.(change);
+        await changeManager.submit(change);
         notify('Feature added successfully', 'success');
         handleClose();
         event.preventDefault();
@@ -1685,7 +1694,7 @@ function AddChildFeature({ changeManager, handleClose, session, sourceAssemblyId
             setShowPhase(false);
         }
     }
-    async function handleChangePhase(e) {
+    function handleChangePhase(e) {
         setErrorMessage('');
         setPhase(e.target.value);
         switch (Number(e.target.value)) {
@@ -1711,8 +1720,12 @@ function AddChildFeature({ changeManager, handleClose, session, sourceAssemblyId
     return (React__default.createElement(Dialog, { open: true, title: "Add new child feature", handleClose: handleClose, maxWidth: false, "data-testid": "add-feature-dialog" },
         React__default.createElement("form", { onSubmit: onSubmit },
             React__default.createElement(DialogContent, { style: { display: 'flex', flexDirection: 'column' } },
-                React__default.createElement(TextField, { margin: "dense", id: "start", label: "Start", type: "number", fullWidth: true, variant: "outlined", value: start, onChange: (e) => setStart(e.target.value) }),
-                React__default.createElement(TextField, { margin: "dense", id: "end", label: "End", type: "number", fullWidth: true, variant: "outlined", value: end, onChange: (e) => setEnd(e.target.value), error: error, helperText: error ? '"End" must be greater than "Start"' : null }),
+                React__default.createElement(TextField, { margin: "dense", id: "start", label: "Start", type: "number", fullWidth: true, variant: "outlined", value: start, onChange: (e) => {
+                        setStart(e.target.value);
+                    } }),
+                React__default.createElement(TextField, { margin: "dense", id: "end", label: "End", type: "number", fullWidth: true, variant: "outlined", value: end, onChange: (e) => {
+                        setEnd(e.target.value);
+                    }, error: error, helperText: error ? '"End" must be greater than "Start"' : null }),
                 React__default.createElement(OntologyTermAutocomplete, { session: session, ontologyName: "Sequence Ontology", style: { width: 170 }, value: type, filterTerms: isOntologyClass, fetchValidTerms: fetchValidTerms.bind(null, sourceFeature), renderInput: (params) => (React__default.createElement(TextField, { ...params, label: "Type", variant: "outlined", fullWidth: true, error: Boolean(typeWarningText), helperText: typeWarningText })), onChange: (oldValue, newValue) => {
                         if (newValue) {
                             handleChangeType(newValue);
@@ -1766,7 +1779,7 @@ function CopyFeature({ changeManager, handleClose, session, sourceAssemblyId, so
     const [selectedRefSeqId, setSelectedRefSeqId] = useState('');
     const [start, setStart] = useState(sourceFeature.start);
     const [errorMessage, setErrorMessage] = useState('');
-    async function handleChangeAssembly(e) {
+    function handleChangeAssembly(e) {
         setSelectedAssemblyId(e.target.value);
     }
     useEffect(() => {
@@ -1790,9 +1803,11 @@ function CopyFeature({ changeManager, handleClose, session, sourceAssemblyId, so
             setRefNames(newRefNames);
             setSelectedRefSeqId(newRefNames[0]?._id || '');
         }
-        getRefNames().catch((error) => setErrorMessage(String(error)));
+        getRefNames().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [selectedAssemblyId, assemblyManager]);
-    async function handleChangeRefSeq(e) {
+    function handleChangeRefSeq(e) {
         const refSeq = e.target.value;
         setSelectedRefSeqId(refSeq);
     }
@@ -1808,7 +1823,7 @@ function CopyFeature({ changeManager, handleClose, session, sourceAssemblyId, so
             setErrorMessage(`Assembly not found: ${selectedAssemblyId}.`);
             return;
         }
-        const canonicalRefName = assembly?.getCanonicalRefName(selectedRefSeqId);
+        const canonicalRefName = assembly.getCanonicalRefName(selectedRefSeqId);
         const region = assembly.regions?.find((r) => r.refName === canonicalRefName);
         if (!region) {
             setErrorMessage(`RefSeq not found: ${selectedRefSeqId}.`);
@@ -1864,7 +1879,7 @@ function CopyFeature({ changeManager, handleClose, session, sourceAssemblyId, so
             copyFeature: true,
             allIds: featureIds,
         });
-        await changeManager.submit?.(change);
+        await changeManager.submit(change);
         notify('Feature copied successfully', 'success');
         handleClose();
         event.preventDefault();
@@ -1924,6 +1939,7 @@ function CopyFeature({ changeManager, handleClose, session, sourceAssemblyId, so
             React__default.createElement(DialogContentText, { color: "error" }, errorMessage))) : null));
 }
 
+/* eslint-disable @typescript-eslint/no-misused-promises */
 function DeleteAssembly({ changeManager, handleClose, session, }) {
     const { internetAccounts } = getRoot(session);
     const [selectedAssembly, setSelectedAssembly] = useState();
@@ -1966,7 +1982,7 @@ function DeleteAssembly({ changeManager, handleClose, session, }) {
             typeName: 'DeleteAssemblyChange',
             assembly: selectedAssembly.name,
         });
-        await changeManager.submit?.(change, {
+        await changeManager.submit(change, {
             internetAccountId: selectedInternetAccount.internetAccountId,
         });
         handleClose();
@@ -1983,7 +1999,9 @@ function DeleteAssembly({ changeManager, handleClose, session, }) {
                 React__default.createElement(DialogContentText, null,
                     React__default.createElement("strong", { style: { color: 'red' } }, "NOTE: All assembly data will be deleted and this operation cannot be undone!")),
                 React__default.createElement(FormGroup, null,
-                    React__default.createElement(FormControlLabel, { control: React__default.createElement(Checkbox, { checked: confirmDelete, onChange: () => setconfirmDelete(!confirmDelete) }), label: "I understand that all assembly data will be deleted" }))),
+                    React__default.createElement(FormControlLabel, { control: React__default.createElement(Checkbox, { checked: confirmDelete, onChange: () => {
+                                setconfirmDelete(!confirmDelete);
+                            } }), label: "I understand that all assembly data will be deleted" }))),
             React__default.createElement(DialogActions, null,
                 React__default.createElement(Button, { disabled: !selectedAssembly || !confirmDelete, variant: "contained", type: "submit" }, "Delete"),
                 React__default.createElement(Button, { variant: "outlined", type: "submit", onClick: handleClose }, "Cancel"))),
@@ -2008,7 +2026,7 @@ function DeleteFeature({ changeManager, handleClose, selectedFeature, session, s
             deletedFeature: getSnapshot(sourceFeature),
             parentFeatureId: sourceFeature.parent?._id,
         });
-        await changeManager.submit?.(change);
+        await changeManager.submit(change);
         notify('Feature deleted successfully', 'success');
         handleClose();
         event.preventDefault();
@@ -2110,7 +2128,7 @@ function DownloadGFF3({ handleClose, session }) {
             });
         }
         for (const [, refSeq] of refSeqs) {
-            const features = refSeq?.features;
+            const { features } = refSeq;
             if (!features) {
                 continue;
             }
@@ -2139,6 +2157,7 @@ function DownloadGFF3({ handleClose, session }) {
             React__default.createElement(DialogContentText, { color: "error" }, errorMessage))) : null));
 }
 
+/* eslint-disable @typescript-eslint/unbound-method */
 function ImportFeatures({ changeManager, handleClose, session, }) {
     const { apolloDataStore } = session;
     const [file, setFile] = useState();
@@ -2180,7 +2199,7 @@ function ImportFeatures({ changeManager, handleClose, session, }) {
                 assemblyId: selectedAssembly.name,
             });
             uri.search = searchParams.toString();
-            const fetch = apolloInternetAccount?.getFetcher({
+            const fetch = apolloInternetAccount.getFetcher({
                 locationType: 'UriLocation',
                 uri: uri.toString(),
             });
@@ -2234,7 +2253,7 @@ function ImportFeatures({ changeManager, handleClose, session, }) {
         formData.append('file', file);
         formData.append('fileName', file.name);
         formData.append('type', 'text/x-gff3');
-        const apolloFetchFile = apolloInternetAccount?.getFetcher({
+        const apolloFetchFile = apolloInternetAccount.getFetcher({
             locationType: 'UriLocation',
             uri: url,
         });
@@ -2329,7 +2348,9 @@ function ManageChecks({ handleClose, session }) {
             const data = (await response.json());
             setChecks(data);
         }
-        getChecks().catch((error) => setErrorMessage(String(error)));
+        getChecks().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [selectedInternetAccount]);
     useEffect(() => {
         if (assemblies.length > 0 && selectedAssembly === undefined) {
@@ -2353,7 +2374,9 @@ function ManageChecks({ handleClose, session }) {
             const assembly = (await response.json());
             setSelectedChecks(assembly.checks);
         }
-        getChecks().catch((error) => setErrorMessage(String(error)));
+        getChecks().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [selectedAssembly, selectedInternetAccount]);
     function handleChangeAssembly(e) {
         const newAssembly = assemblies.find((asm) => asm.name === e.target.value);
@@ -2443,6 +2466,7 @@ function ManageChecks({ handleClose, session }) {
             React__default.createElement(DialogContentText, { color: "error" }, errorMessage))) : null));
 }
 
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 function ManageUsers({ changeManager, handleClose, session, }) {
     const { internetAccounts } = getRoot(session);
     const apolloInternetAccounts = internetAccounts.filter((ia) => ia.type === 'ApolloInternetAccount' && ia.role?.includes('admin'));
@@ -2455,7 +2479,7 @@ function ManageUsers({ changeManager, handleClose, session, }) {
     const getUsers = useCallback(async () => {
         const { baseURL } = selectedInternetAccount;
         const uri = new URL('/users', baseURL).href;
-        const apolloFetch = selectedInternetAccount?.getFetcher({
+        const apolloFetch = selectedInternetAccount.getFetcher({
             locationType: 'UriLocation',
             uri,
         });
@@ -2471,7 +2495,9 @@ function ManageUsers({ changeManager, handleClose, session, }) {
         }
     }, [selectedInternetAccount]);
     useEffect(() => {
-        getUsers().catch((error) => setErrorMessage(String(error)));
+        getUsers().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [getUsers]);
     async function deleteUser(id) {
         const change = new DeleteUserChange({
@@ -2536,13 +2562,16 @@ function ManageUsers({ changeManager, handleClose, session, }) {
                 React__default.createElement(DialogContentText, null, "Select account"),
                 React__default.createElement(Select, { value: selectedInternetAccount.internetAccountId, onChange: handleChangeInternetAccount, disabled: !errorMessage }, internetAccounts.map((option) => (React__default.createElement(MenuItem, { key: option.id, value: option.internetAccountId }, option.name)))))) : null,
             React__default.createElement("div", { style: { height: '100%', width: '100%' } },
-                React__default.createElement(DataGrid, { pagination: true, rows: users, columns: gridColumns, getRowId: (row) => row._id, slots: { toolbar: GridToolbar }, getRowHeight: () => 'auto', isCellEditable: (params) => !isCurrentUser(params.id), processRowUpdate: processRowUpdate, onProcessRowUpdateError: (error) => setErrorMessage(String(error)) }))),
+                React__default.createElement(DataGrid, { pagination: true, rows: users, columns: gridColumns, getRowId: (row) => row._id, slots: { toolbar: GridToolbar }, getRowHeight: () => 'auto', isCellEditable: (params) => !isCurrentUser(params.id), processRowUpdate: processRowUpdate, onProcessRowUpdateError: (error) => {
+                        setErrorMessage(String(error));
+                    } }))),
         React__default.createElement(DialogActions, null,
             React__default.createElement(Button, { variant: "outlined", type: "submit", onClick: handleClose }, "Close")),
         errorMessage ? (React__default.createElement(DialogContent, null,
             React__default.createElement(DialogContentText, { color: "error" }, errorMessage))) : null));
 }
 
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 // interface TermAutocompleteResult extends TermValue {
 //   label: string[]
 //   match: string
@@ -2591,8 +2620,7 @@ function TermTagWithTooltip({ getTagProps, index, ontology, termId, }) {
             React.createElement(Chip, { label: errorMessage || manager.applyPrefixes(termId), color: errorMessage ? 'error' : 'default', size: "small", ...getTagProps({ index }) }))));
 }
 function OntologyTermMultiSelect({ includeDeprecated, onChange, ontologyName, ontologyVersion, session, value: initialValue, }) {
-    const ontologyManager = session.apolloDataStore
-        .ontologyManager;
+    const { ontologyManager } = session.apolloDataStore;
     const ontology = ontologyManager.findOntology(ontologyName, ontologyVersion);
     const [value, setValue] = React.useState(initialValue.map((id) => ({ term: { id, type: 'CLASS' } })));
     const [inputValue, setInputValue] = React.useState('');
@@ -2851,7 +2879,7 @@ function ModifyFeatureAttribute({ changeManager, handleClose, session, sourceAss
             featureId: sourceFeature._id,
             attributes: attrs,
         });
-        await changeManager.submit?.(change);
+        await changeManager.submit(change);
         notify('Feature attributes modified successfully', 'success');
         handleClose();
         event.preventDefault();
@@ -2955,6 +2983,7 @@ function ModifyFeatureAttribute({ changeManager, handleClose, session, sourceAss
                 React__default.createElement(Button, { variant: "outlined", type: "submit", disabled: showAddNewForm, onClick: handleClose }, "Cancel")))));
 }
 
+/* eslint-disable @typescript-eslint/unbound-method */
 function OpenLocalFile({ handleClose, session }) {
     const { addApolloTrackConfig, apolloDataStore } = session;
     const { addAssembly, addSessionAssembly, assemblyManager, notify } = session;
@@ -2963,7 +2992,7 @@ function OpenLocalFile({ handleClose, session }) {
     const [errorMessage, setErrorMessage] = useState('');
     const [submitted, setSubmitted] = useState(false);
     const theme = useTheme();
-    async function handleChangeFile(e) {
+    function handleChangeFile(e) {
         const selectedFile = e.target.files?.item(0);
         if (!selectedFile) {
             return;
@@ -3020,10 +3049,10 @@ function OpenLocalFile({ handleClose, session }) {
         if (a) {
             // @ts-expect-error MST type coercion problem?
             addApolloTrackConfig(a);
-            notify(`Loaded GFF3 ${file?.name}`, 'success');
+            notify(`Loaded GFF3 ${file.name}`, 'success');
         }
         else {
-            notify(`Error loading GFF3 ${file?.name}`, 'error');
+            notify(`Error loading GFF3 ${file.name}`, 'error');
         }
         handleClose();
     }
@@ -3048,6 +3077,7 @@ function OpenLocalFile({ handleClose, session }) {
             React__default.createElement(DialogContentText, { color: "error" }, errorMessage))) : null));
 }
 
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 const useStyles$d = makeStyles()((theme) => ({
     changeTextarea: {
         fontFamily: 'monospace',
@@ -3113,7 +3143,9 @@ function ViewChangeLog({ handleClose, session }) {
                 setAssemblyCollection(data);
             }
         }
-        getAssemblies().catch((error) => setErrorMessage(String(error)));
+        getAssemblies().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [apolloInternetAccount, baseURL]);
     useEffect(() => {
         if (!assemblyId && assemblyCollection.length > 0) {
@@ -3147,9 +3179,11 @@ function ViewChangeLog({ handleClose, session }) {
                 setDisplayGridData(data);
             }
         }
-        getGridData().catch((error) => setErrorMessage(String(error)));
+        getGridData().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [assemblyId, apolloInternetAccount, baseURL]);
-    async function handleChangeAssembly(e) {
+    function handleChangeAssembly(e) {
         setAssemblyId(e.target.value);
     }
     return (React__default.createElement(Dialog, { open: true, fullScreen: true, title: "View change log", handleClose: handleClose, "data-testid": "view-changelog" },
@@ -3206,8 +3240,7 @@ function addMenuItems(rootModel) {
                     handleClose: () => {
                         doneCallback();
                     },
-                    changeManager: session.apolloDataStore
-                        .changeManager,
+                    changeManager: session.apolloDataStore.changeManager,
                 },
             ]);
         },
@@ -3222,8 +3255,7 @@ function addMenuItems(rootModel) {
                     handleClose: () => {
                         doneCallback();
                     },
-                    changeManager: session.apolloDataStore
-                        .changeManager,
+                    changeManager: session.apolloDataStore.changeManager,
                 },
             ]);
         },
@@ -3312,7 +3344,9 @@ const AuthTypeSelector = ({ baseURL, handleClose, name, }) => {
             const data = (await response.json());
             setLoginTypes(data);
         }
-        getAuthTypes().catch((error) => isAbortException(error) ? '' : setErrorMessage(String(error)));
+        getAuthTypes().catch((error) => {
+            isAbortException(error) ? '' : setErrorMessage(String(error));
+        });
         return () => {
             controller.abort();
         };
@@ -3333,11 +3367,17 @@ const AuthTypeSelector = ({ baseURL, handleClose, name, }) => {
     const allowGuest = loginTypes.includes('guest');
     return (React__default.createElement(Dialog, { open: true, title: `Log in to ${name}`, handleClose: handleClose, maxWidth: false, "data-testid": "login-apollo" },
         React__default.createElement(DialogContent, { style: { display: 'flex', flexDirection: 'column', paddingTop: 8 } },
-            allowGoogle ? (React__default.createElement(GoogleButton, { disabled: !allowGoogle, onClick: () => handleClick('google') })) : null,
-            allowMicrosoft ? (React__default.createElement(MicrosoftButton, { disabled: !allowMicrosoft, onClick: () => handleClick('microsoft') })) : null,
+            allowGoogle ? (React__default.createElement(GoogleButton, { disabled: !allowGoogle, onClick: () => {
+                    handleClick('google');
+                } })) : null,
+            allowMicrosoft ? (React__default.createElement(MicrosoftButton, { disabled: !allowMicrosoft, onClick: () => {
+                    handleClick('microsoft');
+                } })) : null,
             allowGuest ? (React__default.createElement(React__default.Fragment, null,
                 React__default.createElement(Divider, { className: classes.divider }),
-                React__default.createElement(GuestButton, { onClick: () => handleClick('guest') }))) : null),
+                React__default.createElement(GuestButton, { onClick: () => {
+                        handleClick('guest');
+                    } }))) : null),
         React__default.createElement(DialogActions, null,
             React__default.createElement(Button, { variant: "outlined", type: "submit", onClick: () => {
                     handleClose();
@@ -3346,6 +3386,7 @@ const AuthTypeSelector = ({ baseURL, handleClose, name, }) => {
             React__default.createElement(DialogContentText, { color: "error" }, errorMessage))) : null));
 };
 
+/* eslint-disable @typescript-eslint/no-unused-vars */
 const inWebWorker$1 = typeof sessionStorage === 'undefined';
 const stateModelFactory$2 = (configSchema) => {
     return InternetAccount.named('ApolloInternetAccount')
@@ -3397,8 +3438,6 @@ const stateModelFactory$2 = (configSchema) => {
         return {
             addMessageChannel(resolve, reject) {
                 listener = (event) => {
-                    // this should probably get better handling, but ignored for now
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     this.finishOAuthWindow(event, resolve, reject);
                 };
                 window.addEventListener('message', listener);
@@ -3406,9 +3445,10 @@ const stateModelFactory$2 = (configSchema) => {
             deleteMessageChannel() {
                 window.removeEventListener('message', listener);
             },
-            async finishOAuthWindow(event, resolve, reject) {
+            finishOAuthWindow(event, resolve, reject) {
                 if (event.data.name !== `JBrowseAuthWindow-${self.internetAccountId}`) {
-                    return this.deleteMessageChannel();
+                    this.deleteMessageChannel();
+                    return;
                 }
                 const redirectUriWithInfo = event.data.redirectUri;
                 const fixedQueryString = redirectUriWithInfo.replace('#', '?');
@@ -3418,11 +3458,12 @@ const stateModelFactory$2 = (configSchema) => {
                 const token = urlParams.get('access_token');
                 this.deleteMessageChannel();
                 if (!token) {
-                    return reject(new Error('Error with token endpoint'));
+                    reject(new Error('Error with token endpoint'));
+                    return;
                 }
                 self.storeToken(token);
                 self.setRole();
-                return resolve(token);
+                resolve(token);
             },
             async openAuthWindow(type, resolve, reject) {
                 const redirectUri = isElectron
@@ -3445,7 +3486,6 @@ const stateModelFactory$2 = (configSchema) => {
                     const eventFromDesktop = new MessageEvent('message', {
                         data: { name: eventName, redirectUri: redirectUriFromElectron },
                     });
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
                     this.finishOAuthWindow(eventFromDesktop, resolve, reject);
                 }
                 else {
@@ -3493,7 +3533,8 @@ const stateModelFactory$2 = (configSchema) => {
             const response = await fetch(uri);
             if (!response.ok) {
                 const errorMessage = await createFetchErrorMessage(response, 'Error when logging in');
-                return reject(new Error(errorMessage));
+                reject(new Error(errorMessage));
+                return;
             }
             const { token } = await response.json();
             resolve(token);
@@ -3529,8 +3570,7 @@ const stateModelFactory$2 = (configSchema) => {
         }),
         getMissingChanges: flow(function* getMissingChanges() {
             const { session } = getRoot(self);
-            const { changeManager } = session
-                .apolloDataStore;
+            const { changeManager } = session.apolloDataStore;
             if (!self.lastChangeSequenceNumber) {
                 throw new Error('No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server');
             }
@@ -3554,7 +3594,7 @@ const stateModelFactory$2 = (configSchema) => {
             const serializedChanges = yield response.json();
             for (const serializedChange of serializedChanges) {
                 const change = Change.fromJSON(serializedChange);
-                void changeManager?.submit(change, { submitToBackend: false });
+                void changeManager.submit(change, { submitToBackend: false });
             }
         }),
     }))
@@ -3593,7 +3633,7 @@ const stateModelFactory$2 = (configSchema) => {
                     return; // we did this change, no need to apply it again
                 }
                 const change = Change.fromJSON(message.changeInfo);
-                void changeManager?.submit(change, { submitToBackend: false });
+                void changeManager.submit(change, { submitToBackend: false });
             });
             socket.on('USER_LOCATION', (message) => {
                 const { channel, locations, userName, userSessionId } = message;
@@ -3648,7 +3688,9 @@ const stateModelFactory$2 = (configSchema) => {
             let timeoutId;
             return (userLocation) => {
                 clearTimeout(timeoutId);
-                timeoutId = setTimeout(() => fn(userLocation), debounceTimeout);
+                timeoutId = setTimeout(() => {
+                    fn(userLocation);
+                }, debounceTimeout);
             };
         };
         return { postUserLocation: debouncePostUserLocation(postUserLocation) };
@@ -3705,6 +3747,7 @@ const stateModelFactory$2 = (configSchema) => {
     }));
 };
 
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 function isApolloMessageData$1(data) {
     return (typeof data === 'object' &&
         data !== null &&
@@ -3893,8 +3936,9 @@ function ApolloRendering(props) {
     const { session } = displayModel;
     const { collaborators: collabs } = session;
     // bridging mobx observability and React useEffect observability
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    useEffect(() => autorun(() => setCollaborators(toJS(collabs))), []);
+    useEffect(() => autorun(() => {
+        setCollaborators(toJS(collabs));
+    }), []);
     const [region] = regions;
     const totalWidth = (region.end - region.start) / bpPerPx;
     const { apolloFeatureUnderMouse, apolloRowHeight: height, apolloRowUnderMouse, changeManager, codonLayout, featureLayout, features, featuresHeight: totalHeight, getAssemblyId, selectedFeature, setApolloFeatureUnderMouse, setApolloRowUnderMouse, setSelectedFeature, showIntronLines: showLines, showStartCodons: showStarts, showStopCodons: showStops, } = displayModel;
@@ -4275,7 +4319,7 @@ function ApolloRendering(props) {
                     assembly,
                 });
             }
-            await changeManager?.submit(change);
+            await changeManager.submit(change);
         }
         // eslint-disable-next-line unicorn/no-useless-undefined
         setDragging(undefined);
@@ -4376,6 +4420,7 @@ var ApolloSixFrameRendererReactComponent = observer(ApolloRendering);
 
 var apolloSixFrameRendererConfigSchema = ConfigurationSchema('ApolloSixFrameRenderer', {}, { explicitlyTyped: true });
 
+/* eslint-disable @typescript-eslint/require-await */
 class ApolloSixFrameRenderer extends RendererType {
     async renderInClient(_rpcManager, args) {
         return this.render(args);
@@ -4385,6 +4430,7 @@ class ApolloSixFrameRenderer extends RendererType {
     }
 }
 
+/* eslint-disable @typescript-eslint/no-unsafe-return */
 class ApolloTextSearchAdapter extends BaseAdapter {
     get baseURL() {
         return readConfObject(this.config, 'baseURL').uri;
@@ -4449,6 +4495,7 @@ function installApolloTextSearchAdapter(pluginManager) {
     }));
 }
 
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 var PhaseEnum;
 (function (PhaseEnum) {
     PhaseEnum[PhaseEnum["zero"] = 0] = "zero";
@@ -4502,7 +4549,7 @@ function AddFeature({ changeManager, handleClose, region, session, }) {
                 strand,
             },
         });
-        await changeManager.submit?.(change);
+        await changeManager.submit(change);
         notify('Feature added successfully', 'success');
         handleClose();
         event.preventDefault();
@@ -4535,7 +4582,7 @@ function AddFeature({ changeManager, handleClose, region, session, }) {
             }
         }
     }
-    async function handleChangePhase(e) {
+    function handleChangePhase(e) {
         setErrorMessage('');
         setPhase(e.target.value);
         switch (Number(e.target.value)) {
@@ -4561,8 +4608,12 @@ function AddFeature({ changeManager, handleClose, region, session, }) {
     return (React__default.createElement(Dialog, { open: true, title: "Add new feature", handleClose: handleClose, maxWidth: false, "data-testid": "add-feature-dialog" },
         React__default.createElement("form", { onSubmit: onSubmit },
             React__default.createElement(DialogContent, { style: { display: 'flex', flexDirection: 'column' } },
-                React__default.createElement(TextField, { margin: "dense", id: "start", label: "Start", type: "number", fullWidth: true, variant: "outlined", value: Number(start), onChange: (e) => setStart(e.target.value) }),
-                React__default.createElement(TextField, { margin: "dense", id: "end", label: "End", type: "number", fullWidth: true, variant: "outlined", value: end, onChange: (e) => setEnd(e.target.value), error: error, helperText: error ? '"End" must be greater than "Start"' : null }),
+                React__default.createElement(TextField, { margin: "dense", id: "start", label: "Start", type: "number", fullWidth: true, variant: "outlined", value: Number(start), onChange: (e) => {
+                        setStart(e.target.value);
+                    } }),
+                React__default.createElement(TextField, { margin: "dense", id: "end", label: "End", type: "number", fullWidth: true, variant: "outlined", value: end, onChange: (e) => {
+                        setEnd(e.target.value);
+                    }, error: error, helperText: error ? '"End" must be greater than "Start"' : null }),
                 React__default.createElement(OntologyTermAutocomplete, { session: session, ontologyName: "Sequence Ontology", style: { width: 170 }, value: type, filterTerms: isOntologyClass, renderInput: (params) => (React__default.createElement(TextField, { ...params, label: "Type", variant: "outlined", fullWidth: true })), onChange: (oldValue, newValue) => {
                         if (newValue) {
                             handleChangeType(newValue);
@@ -4642,7 +4693,9 @@ function ViewCheckResults({ handleClose, session, }) {
                 setDisplayGridData(data);
             }
         }
-        getGridData().catch((error) => setErrorMessage(String(error)));
+        getGridData().catch((error) => {
+            setErrorMessage(String(error));
+        });
     }, [selectedAssembly, apolloInternetAccount, baseURL]);
     function handleChangeAssembly(e) {
         const newAssembly = assemblies.find((asm) => asm.name === e.target.value);
@@ -4795,7 +4848,7 @@ function annotationFromPileup(pluggableElement) {
                 cdsFeature.start = Math.min(cdsFeature.start, exon.start);
                 cdsFeature.end = Math.max(cdsFeature.end, exon.end);
                 const { end, start } = exon;
-                discontinuousLocations?.push({ start, end, phase });
+                discontinuousLocations.push({ start, end, phase });
                 const localPhase = (end - start) % 3;
                 phase = ((phase + localPhase) % 3);
                 const newExon = {
@@ -4823,7 +4876,7 @@ function annotationFromPileup(pluggableElement) {
                 addedFeature: newFeature,
             });
             const session = getSession(self);
-            await session.apolloDataStore.changeManager.submit?.(change);
+            await session.apolloDataStore.changeManager.submit(change);
             session.notify('Annotation added successfully', 'success');
         },
     }))
@@ -4850,6 +4903,7 @@ function annotationFromPileup(pluggableElement) {
     return pluggableElement;
 }
 
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 const StringTextField = observer(function StringTextField({ onChangeCommitted, value: initialValue, ...props }) {
     const [value, setValue] = useState(String(initialValue));
     const [blur, setBlur] = useState(false);
@@ -4878,7 +4932,9 @@ const StringTextField = observer(function StringTextField({ onChangeCommitted, v
             if (value !== String(initialValue)) {
                 onChangeCommitted(value);
             }
-        }, inputRef: (node) => setInputNode(node) }));
+        }, inputRef: (node) => {
+            setInputNode(node);
+        } }));
 });
 
 const reservedKeys = new Map([
@@ -5015,7 +5071,7 @@ const Attributes = observer(function Attributes({ assembly, editable, feature, s
             featureId: feature._id,
             attributes: attrs,
         });
-        await changeManager.submit?.(change);
+        await changeManager.submit(change);
         notify('Feature attributes modified successfully', 'success');
     }
     function handleAddNewAttributeChange() {
@@ -5098,6 +5154,7 @@ const Attributes = observer(function Attributes({ assembly, editable, feature, s
         errorMessage ? (React__default.createElement(Typography, { color: "error" }, errorMessage)) : null));
 });
 
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
 const NumberTextField = observer(function NumberTextField({ onChangeCommitted, value: initialValue, ...props }) {
     const [value, setValue] = useState(String(initialValue));
     const [blur, setBlur] = useState(false);
@@ -5133,14 +5190,18 @@ const NumberTextField = observer(function NumberTextField({ onChangeCommitted, v
                     onChangeCommitted(valueAsNumber);
                 }
             }
-        }, inputRef: (node) => setInputNode(node), error: error, helperText: error ? 'Not a valid number' : undefined }));
+        }, inputRef: (node) => {
+            setInputNode(node);
+        }, error: error, helperText: error ? 'Not a valid number' : undefined }));
 });
 
 const BasicInformation = observer(function BasicInformation({ assembly, feature, session, }) {
     const [errorMessage, setErrorMessage] = useState('');
     const [typeWarningText, setTypeWarningText] = useState('');
     const { _id, assemblyId, end, start, strand, type } = feature;
-    const notifyError = (e) => session.notify(e.message, 'error');
+    const notifyError = (e) => {
+        session.notify(e.message, 'error');
+    };
     const { changeManager } = session.apolloDataStore;
     function handleTypeChange(newType) {
         setErrorMessage('');
@@ -5236,7 +5297,7 @@ const RelatedFeatures = observer(function RelatedFeatures({ assembly, feature, r
                 assembly,
                 refName,
             });
-            session.showWidget?.(apolloFeatureWidget);
+            session.showWidget(apolloFeatureWidget);
         }
     };
     if (!(parent || (children && children.size > 0))) {
@@ -5248,12 +5309,16 @@ const RelatedFeatures = observer(function RelatedFeatures({ assembly, feature, r
             React__default.createElement(Typography, { variant: "h5" }, "Parent"),
             React__default.createElement(Paper, { elevation: 6, className: classes.paper },
                 `Start: ${parent.start}, End: ${parent.end}, Type: ${parent.type}`,
-                React__default.createElement(Button, { variant: "contained", onClick: () => onButtonClick(parent) }, "Go to parent")))),
+                React__default.createElement(Button, { variant: "contained", onClick: () => {
+                        onButtonClick(parent);
+                    } }, "Go to parent")))),
         children && children.size > 0 && (React__default.createElement(React__default.Fragment, null,
             React__default.createElement(Typography, { variant: "h5" }, "Children"),
             [...children.values()].map((child) => (React__default.createElement(Paper, { elevation: 6, className: classes.paper, key: child._id },
                 `Start: ${child.start}, End: ${child.end}, Type: ${child.type}`,
-                React__default.createElement(Button, { variant: "contained", onClick: () => onButtonClick(child) }, "Go to child"))))))));
+                React__default.createElement(Button, { variant: "contained", onClick: () => {
+                        onButtonClick(child);
+                    } }, "Go to child"))))))));
 });
 
 function formatSequence(seq, refName, start, end, wrap) {
@@ -5341,6 +5406,7 @@ const ApolloFeatureDetailsWidget = observer(function ApolloFeatureDetailsWidget(
         React__default.createElement(RelatedFeatures, { feature: feature, refName: refName, session: session, assembly: currentAssembly._id })));
 });
 
+/* eslint-disable @typescript-eslint/no-unsafe-call */
 const ApolloFeatureDetailsWidgetModel = types
     .model('ApolloFeatureDetailsWidget', {
     id: ElementId,
@@ -5623,7 +5689,9 @@ const NumberCell = observer(function NumberCell({ initialValue, notifyError, onC
                 if (value !== initialValue) {
                     onChangeCommitted(value).catch(notifyError);
                 }
-            }, ref: (node) => setInputNode(node) })));
+            }, ref: (node) => {
+                setInputNode(node);
+            } })));
 });
 
 const useStyles$4 = makeStyles()((theme) => ({
@@ -5682,7 +5750,9 @@ const Feature = observer(function Feature({ depth, feature, isHovered, isSelecte
         tabularEditorState.setFeatureCollapsed(_id, expanded);
     };
     // pop up a snackbar in the session notifying user of an error
-    const notifyError = (e) => session.notify(e.message, 'error');
+    const notifyError = (e) => {
+        session.notify(e.message, 'error');
+    };
     return (React__default.createElement(React__default.Fragment, null,
         React__default.createElement("tr", { onMouseEnter: (_e) => {
                 displayState.setApolloHover({
@@ -5844,6 +5914,7 @@ const HybridGrid = observer(function HybridGrid({ model, }) {
             }, style: { zIndex: theme.zIndex.tooltip }, menuItems: contextMenu?.items ?? [], anchorReference: "anchorPosition", anchorPosition: contextMenu?.position })));
 });
 
+/* eslint-disable @typescript-eslint/unbound-method */
 const useStyles$2 = makeStyles()({
     toolbar: {
         width: '100%',
@@ -5863,9 +5934,13 @@ const ToolBar = observer(function ToolBar({ model: displayState, }) {
         React__default.createElement(Tooltip, { title: "Collapse all" },
             React__default.createElement(IconButton, { "aria-label": "collapse", sx: { marginTop: 0 }, onClick: model.collapseAllFeatures },
                 React__default.createElement(UnfoldLessIcon, null))),
-        React__default.createElement(TextField, { className: classes.filterText, label: "Filter features", value: model.filterText, sx: { marginTop: 0 }, variant: "outlined", onChange: (event) => model.setFilterText(event.target.value), InputProps: {
+        React__default.createElement(TextField, { className: classes.filterText, label: "Filter features", value: model.filterText, sx: { marginTop: 0 }, variant: "outlined", onChange: (event) => {
+                model.setFilterText(event.target.value);
+            }, InputProps: {
                 endAdornment: (React__default.createElement(InputAdornment$1, { position: "end" },
-                    React__default.createElement(IconButton, { onClick: () => model.clearFilterText() },
+                    React__default.createElement(IconButton, { onClick: () => {
+                            model.clearFilterText();
+                        } },
                         React__default.createElement(ClearIcon, null)))),
             } })));
 });
@@ -6167,7 +6242,7 @@ class Glyph {
                         assembly: currentAssemblyId,
                         refName: region.refName,
                     });
-                    session.showWidget?.(apolloFeatureWidget);
+                    session.showWidget(apolloFeatureWidget);
                 },
             });
         }
@@ -6581,7 +6656,7 @@ function baseModelFactory(_pluginManager, configSchema) {
         },
         get changeManager() {
             return self.session.apolloDataStore
-                ?.changeManager;
+                .changeManager;
         },
         getAssemblyId(assemblyName) {
             const { assemblyManager } = self.session;
@@ -6598,7 +6673,7 @@ function baseModelFactory(_pluginManager, configSchema) {
     }))
         .actions((self) => ({
         setSelectedFeature(feature) {
-            return self.session.apolloSetSelectedFeature(feature);
+            self.session.apolloSetSelectedFeature(feature);
         },
         afterAttach() {
             addDisposer(self, autorun(() => {
@@ -6893,8 +6968,8 @@ function codonColorCode(letter, rowColorCode, bpPerPx) {
         M: '#33ee33',
         '*': '#f44336',
     };
-    if (colorMap[letter?.toUpperCase()] !== undefined) {
-        return colorMap[letter?.toUpperCase()];
+    if (colorMap[letter.toUpperCase()] !== undefined) {
+        return colorMap[letter.toUpperCase()];
     }
     return bpPerPx <= 0.1 ? rowColorCode : 'lightgray';
 }
@@ -7274,7 +7349,7 @@ class CanonicalGeneGlyph extends Glyph {
                 let featureRow;
                 let i = 0;
                 for (const [, f] of children ?? new Map()) {
-                    if (f._id === apolloSelectedFeature?._id) {
+                    if (f._id === apolloSelectedFeature._id) {
                         featureEntry = f;
                         featureRow = i;
                     }
@@ -7343,7 +7418,7 @@ class CanonicalGeneGlyph extends Glyph {
         let featureRow;
         let i = 0;
         for (const [, f] of topLevelFeature.children ?? new Map()) {
-            if (f._id === feature?._id) {
+            if (f._id === feature._id) {
                 featureEntry = f;
                 featureRow = i;
             }
@@ -7705,10 +7780,10 @@ class CanonicalGeneGlyph extends Glyph {
         }
         if (feature.type !== 'CDS') {
             const adjacentExons = this.adjacentExonsOfExon(feature, topLevelFeature);
-            if (adjacentExons?.nextExon && bp >= adjacentExons?.nextExon.start - 1) {
+            if (adjacentExons?.nextExon && bp >= adjacentExons.nextExon.start - 1) {
                 return;
             }
-            if (adjacentExons?.prevExon && bp <= adjacentExons?.prevExon.end + 1) {
+            if (adjacentExons?.prevExon && bp <= adjacentExons.prevExon.end + 1) {
                 return;
             }
             const dls = this.cdsDlsForExon(feature, topLevelFeature);
@@ -7982,7 +8057,7 @@ class GenericChildGlyph extends BoxGlyph {
     }
     getFeatureFromLayout(feature, bp, row) {
         const layoutRow = this.featuresForRow(feature)[row];
-        return layoutRow?.find((f) => bp >= f.start && bp <= f.end);
+        return layoutRow.find((f) => bp >= f.start && bp <= f.end);
     }
     getRowForFeature(feature, childFeature) {
         const rows = this.featuresForRow(feature);
@@ -8142,7 +8217,7 @@ class ImplicitExonGeneGlyph extends Glyph {
                 let featureRow;
                 let i = 0;
                 for (const [, f] of children ?? new Map()) {
-                    if (f._id === apolloSelectedFeature?._id) {
+                    if (f._id === apolloSelectedFeature._id) {
                         featureEntry = f;
                         featureRow = i;
                     }
@@ -8400,7 +8475,7 @@ class ImplicitExonGeneGlyph extends Glyph {
     }
     getFeatureFromLayout(feature, bp, row) {
         const layoutRow = this.featuresForRow(feature)[row];
-        return layoutRow?.find((f) => bp >= f.start && bp <= f.end);
+        return layoutRow.find((f) => bp >= f.start && bp <= f.end);
     }
     getRowForFeature(feature, childFeature) {
         const rows = this.featuresForRow(feature);
@@ -8639,7 +8714,7 @@ function mouseEventsSeqHightlightModelFactory(pluginManager, configSchema) {
     const LinearApolloDisplayRendering = mouseEventsModelIntermediateFactory(pluginManager, configSchema);
     return LinearApolloDisplayRendering.actions((self) => ({
         afterAttach() {
-            addDisposer(self, autorun(async () => {
+            addDisposer(self, autorun(() => {
                 if (!self.lgv.initialized || self.regionCannotBeRendered()) {
                     return;
                 }
@@ -8884,6 +8959,7 @@ function stateModelFactory$1(pluginManager, configSchema) {
         .named('LinearApolloDisplay');
 }
 
+/* eslint-disable @typescript-eslint/unbound-method */
 const useStyles$1 = makeStyles()((theme) => ({
     canvasContainer: {
         position: 'relative',
@@ -8909,7 +8985,9 @@ const LinearApolloDisplay = observer(function LinearApolloDisplay(props) {
     const { apolloRowHeight, contextMenuItems: getContextMenuItems, cursor, featuresHeight, isShown, onMouseDown, onMouseLeave, onMouseMove, onMouseUp, regionCannotBeRendered, session, setCanvas, setCollaboratorCanvas, setOverlayCanvas, setSeqTrackCanvas, setSeqTrackOverlayCanvas, setTheme, tabularEditor, } = model;
     const { classes } = useStyles$1();
     const lgv = getContainingView(model);
-    useEffect(() => setTheme(theme), [theme, setTheme]);
+    useEffect(() => {
+        setTheme(theme);
+    }, [theme, setTheme]);
     const [contextCoord, setContextCoord] = useState();
     const [contextMenuItems, setContextMenuItems] = useState([]);
     const message = regionCannotBeRendered();
@@ -8968,7 +9046,7 @@ const LinearApolloDisplay = observer(function LinearApolloDisplay(props) {
                 const assembly = assemblyManager.get(region.assemblyName);
                 return [...session.apolloDataStore.checkResults.values()]
                     .filter((checkResult) => assembly?.isValidRefName(checkResult.refSeq) &&
-                    assembly?.getCanonicalRefName(checkResult.refSeq) ===
+                    assembly.getCanonicalRefName(checkResult.refSeq) ===
                         region.refName &&
                     doesIntersect2(region.start, region.end, checkResult.start, checkResult.end))
                     .map((checkResult) => {
@@ -9108,7 +9186,9 @@ const DisplayComponent = observer(function DisplayComponent({ model, ...other })
         model.setDetailsHeight(model.detailsHeight - delta);
     };
     const canvasScrollContainerRef = useRef(null);
-    useEffect(() => scrollSelectedFeatureIntoView(model, canvasScrollContainerRef), [model, selectedFeature]);
+    useEffect(() => {
+        scrollSelectedFeatureIntoView(model, canvasScrollContainerRef);
+    }, [model, selectedFeature]);
     return (React__default.createElement("div", { className: classes.details, style: { height: overallHeight } },
         React__default.createElement(AccordionControl, { open: isShown, title: "Graphical", onClick: toggleShown }),
         React__default.createElement("div", { className: classes.shading, ref: canvasScrollContainerRef, style: { height: featureAreaHeight } },
@@ -9140,6 +9220,7 @@ function makeSixFrameDisplayComponent(pluginManager) {
     return observer(ApolloDisplayComponent);
 }
 
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 const ApolloJobModel = types
     .model('JobsManager', {})
     .views((self) => ({
@@ -9227,6 +9308,7 @@ class BackendDriver {
     }
 }
 
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 class ChangeManager {
     dataStore;
     constructor(dataStore) {
@@ -9338,6 +9420,7 @@ class ChangeManager {
     }
 }
 
+/* eslint-disable @typescript-eslint/no-base-to-string */
 class CollaborationServerDriver extends BackendDriver {
     inFlight = new Map();
     async fetch(internetAccount, info, init) {
@@ -9396,7 +9479,7 @@ class CollaborationServerDriver extends BackendDriver {
             const errorMessage = await createFetchErrorMessage(response, 'getFeatures failed');
             throw new Error(errorMessage);
         }
-        await this.checkSocket(assemblyName, refName, internetAccount);
+        this.checkSocket(assemblyName, refName, internetAccount);
         return response.json();
     }
     /**
@@ -9405,7 +9488,7 @@ class CollaborationServerDriver extends BackendDriver {
      * @param refSeq - refSeqName
      * @param internetAccount - internet account
      */
-    async checkSocket(assembly, refSeq, internetAccount) {
+    checkSocket(assembly, refSeq, internetAccount) {
         const { socket } = internetAccount;
         const token = internetAccount.retrieveToken();
         const channel = `${assembly}-${refSeq}`;
@@ -9448,7 +9531,7 @@ class CollaborationServerDriver extends BackendDriver {
         if (!apolloAssembly) {
             apolloAssembly = this.clientStore.addAssembly(assemblyName);
         }
-        let apolloRefSeq = apolloAssembly?.refSeqs.get(refSeq);
+        let apolloRefSeq = apolloAssembly.refSeqs.get(refSeq);
         if (!apolloRefSeq) {
             apolloRefSeq = apolloAssembly.addRefSeq(refSeq, refName);
         }
@@ -9469,7 +9552,7 @@ class CollaborationServerDriver extends BackendDriver {
         const seqPromise = this.getSeqFromServer(internetAccount, uri, apolloRefSeq, start, end);
         this.inFlight.set(inFlightKey, seqPromise);
         const seq = await seqPromise;
-        await this.checkSocket(assemblyName, refName, internetAccount);
+        this.checkSocket(assemblyName, refName, internetAccount);
         this.inFlight.delete(inFlightKey);
         return { seq, refSeq };
     }
@@ -9607,6 +9690,7 @@ class InMemoryFileDriver extends BackendDriver {
     }
 }
 
+/* eslint-disable @typescript-eslint/require-await */
 class DesktopFileDriver extends BackendDriver {
     async loadAssembly(assemblyName) {
         const { assemblyManager } = getSession(this.clientStore);
@@ -10321,7 +10405,7 @@ function stateModelFactory(pluginManager, configSchema) {
         },
         get changeManager() {
             const session = getSession(self);
-            return session.apolloDataStore?.changeManager;
+            return session.apolloDataStore.changeManager;
         },
         get sequence() {
             const { regions } = self;
@@ -10515,7 +10599,7 @@ function stateModelFactory(pluginManager, configSchema) {
         .actions((self) => ({
         setSelectedFeature(feature) {
             const session = getSession(self);
-            return session.apolloSetSelectedFeature(feature);
+            session.apolloSetSelectedFeature(feature);
         },
         setApolloFeatureUnderMouse(feature) {
             self.apolloFeatureUnderMouse = feature;
@@ -10552,25 +10636,32 @@ function stateModelFactory(pluginManager, configSchema) {
                     label: 'Show start codons',
                     type: 'checkbox',
                     checked: self.showStartCodons,
-                    onClick: () => self.toggleShowStartCodons(),
+                    onClick: () => {
+                        self.toggleShowStartCodons();
+                    },
                 },
                 {
                     label: 'Show stop codons',
                     type: 'checkbox',
                     checked: self.showStopCodons,
-                    onClick: () => self.toggleShowStopCodons(),
+                    onClick: () => {
+                        self.toggleShowStopCodons();
+                    },
                 },
                 {
                     label: 'Show intron lines',
                     type: 'checkbox',
                     checked: self.showIntronLines,
-                    onClick: () => self.toggleShowIntronLines(),
+                    onClick: () => {
+                        self.toggleShowIntronLines();
+                    },
                 },
             ];
         },
     }));
 }
 
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 function isApolloMessageData(data) {
     return (typeof data === 'object' &&
         data !== null &&